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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1Overlapper.html">Overlapper</a></li>  </ul>
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<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
<a href="classclaragenomics_1_1Overlapper-members.html">List of all members</a>  </div>
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<div class="title">claragenomics::Overlapper Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudamapper.html">CUDA mapper package</a></div></div>  </div>
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<p><a class="el" href="classclaragenomics_1_1Overlapper.html" title="Overlapper - given anchors and a read index, calculates overlaps between reads.">Overlapper</a> - given anchors and a read index, calculates overlaps between reads.  
 <a href="classclaragenomics_1_1Overlapper.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="overlapper_8hpp_source.html">overlapper.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ga71e857fe517ae3205844b10b512e4dae"><td class="memItemLeft" align="right" valign="top">
virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga71e857fe517ae3205844b10b512e4dae">~Overlapper</a> ()=default</td></tr>
<tr class="memdesc:ga71e857fe517ae3205844b10b512e4dae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1Overlapper.html" title="Overlapper - given anchors and a read index, calculates overlaps between reads.">Overlapper</a>. <br /></td></tr>
<tr class="separator:ga71e857fe517ae3205844b10b512e4dae"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga07088dbdb8bdbc5f03cdc7a51e22429d"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga07088dbdb8bdbc5f03cdc7a51e22429d">get_overlaps</a> (std::vector&lt; <a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps, std::vector&lt; <a class="el" href="structclaragenomics_1_1Anchor.html">Anchor</a> &gt; &amp;anchors, const <a class="el" href="classclaragenomics_1_1Index.html">Index</a> &amp;index)=0</td></tr>
<tr class="memdesc:ga07088dbdb8bdbc5f03cdc7a51e22429d"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns overlaps for a set of reads  <a href="group__cudamapper.html#ga07088dbdb8bdbc5f03cdc7a51e22429d">More...</a><br /></td></tr>
<tr class="separator:ga07088dbdb8bdbc5f03cdc7a51e22429d"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
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static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga6097f8a81a043b36b23bddf457a7655f">print_paf</a> (const std::vector&lt; <a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps)</td></tr>
<tr class="memdesc:ga6097f8a81a043b36b23bddf457a7655f"><td class="mdescLeft">&#160;</td><td class="mdescRight">prints overlaps to stdout in <a href="https://github.com/lh3/miniasm/blob/master/PAF.md">PAF format</a> <br /></td></tr>
<tr class="separator:ga6097f8a81a043b36b23bddf457a7655f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1df890820b77a1a235394d46f665683e"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga1df890820b77a1a235394d46f665683e">filter_overlaps</a> (std::vector&lt; <a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> &gt; &amp;filtered_overlaps, const std::vector&lt; <a class="el" href="structclaragenomics_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps, size_t min_residues=5, size_t min_overlap_len=0)</td></tr>
<tr class="memdesc:ga1df890820b77a1a235394d46f665683e"><td class="mdescLeft">&#160;</td><td class="mdescRight">removes overlaps which are unlikely to be true overlaps  <a href="group__cudamapper.html#ga1df890820b77a1a235394d46f665683e">More...</a><br /></td></tr>
<tr class="separator:ga1df890820b77a1a235394d46f665683e"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classclaragenomics_1_1Overlapper.html" title="Overlapper - given anchors and a read index, calculates overlaps between reads.">Overlapper</a> - given anchors and a read index, calculates overlaps between reads. </p>
</div><hr/>The documentation for this class was generated from the following file:<ul>
<li>cudamapper/include/cudamapper/<a class="el" href="overlapper_8hpp_source.html">overlapper.hpp</a></li>
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